3SEM

SEM5 SH3 DOMAIN COMPLEXED WITH PEPTOID INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Exploiting the basis of proline recognition by SH3 and WW domains: design of N-substituted inhibitors.

Nguyen, J.T.Turck, C.W.Cohen, F.E.Zuckermann, R.N.Lim, W.A.

(1998) Science 282: 2088-2092

  • DOI: 10.1126/science.282.5396.2088
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Src homology 3 (SH3) and WW protein interaction domains bind specific proline-rich sequences. However, instead of recognizing critical prolines on the basis of side chain shape or rigidity, these domains broadly accepted amide N-substituted residues. ...

    Src homology 3 (SH3) and WW protein interaction domains bind specific proline-rich sequences. However, instead of recognizing critical prolines on the basis of side chain shape or rigidity, these domains broadly accepted amide N-substituted residues. Proline is apparently specifically selected in vivo, despite low complementarity, because it is the only endogenous N-substituted amino acid. This discriminatory mechanism explains how these domains achieve specific but low-affinity recognition, a property that is necessary for transient signaling interactions. The mechanism can be exploited: screening a series of ligands in which key prolines were replaced by nonnatural N-substituted residues yielded a ligand that selectively bound the Grb2 SH3 domain with 100 times greater affinity.


    Organizational Affiliation

    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SEX MUSCLE ABNORMAL PROTEIN 5
A, B
60Caenorhabditis elegansMutation(s): 0 
Gene Names: sem-5C14F5.5
Find proteins for P29355 (Caenorhabditis elegans)
Go to UniProtKB:  P29355
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SH3 PEPTOID INHIBITOR
C, D
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NMC
Query on NMC
C,D
L-PEPTIDE LINKINGC6 H11 N O2GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.05α = 90
b = 68.53β = 93.86
c = 35.02γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-06
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance